Wednesday, July 31, 2013

Large cetacean carcasses at the deep-sea floor, known as ‘whale falls’, provide a resource for generalist-scavenging species, chemosynthetic fauna related to those from hydrothermal vents and cold seeps, and remarkable bone-specialist species such as Osedax worms. Here we report the serendipitous discovery of a late-stage natural whale fall at a depth of 1444 m in the South Sandwich Arc. This discovery represents the first natural whale fall to be encountered in the Southern Ocean, where cetaceans are abundant. The skeleton was situated within a seafloor caldera, in close proximity (<250 m) to active hydrothermal vents. We used a DNA Barcoding approach to identify the skeleton as that of an Antarctic minke whale (Balaenoptera bonaerensis). The carcass was in an advanced state of decomposition, and its exposed bones were occupied by a diverse assemblage of fauna including nine undescribed species. These bone fauna included an undescribed species of Lepetodrilus limpet that was also present at the nearby hydrothermal vents, suggesting the use of whale-fall habitats as stepping stones between chemosynthetic ecosystems. Using Remotely Operated Vehicle (ROV) videography, we have quantified the composition and abundance of fauna on the whale bones, and tested a hypothesis that varying concentrations of lipids in the bones of whales may influence the microdistribution of sulfophilic whale-fall fauna.

This text is from the abstract of a new paper now published in Deep Sea Research Part II. Well, first of all they did not do DNA Barcoding. The complete cytochrome b gene and a part of a tRNA coding region are good DNA identification markers for this particular study but that's not what we call DNA Barcoding.

Enough of the caviling as the study is actually pretty cool. I remember some great footage presented in the BBC series "Blue Planet" which ran 11 years ago. The crew filmed a grey whale carcass in deep water and showed how it was consumed by hagfish, sleeper sharks, and a variety of invertebrates such as crabs. The filming crew did not come across this carcass by chance but instead they used one of a stranded whale and sank it at a different location they revisited for a number of times to film all scavengers that come to feed on it. A year and a half later the carcass was stripped to the bone. This new study could be viewed as the scientific sequel to that initial footage as the researchers look at the skeleton of a minke whale (Balaenoptera bonaerensis) and the organisms that inhabit the bones. The whale species identity was confirmed using DNA and the inhabiting organisms were identified based on ROV video material (see image).

This was the first natural whale fall to be observed in the Southern Ocean, despite this area harbouring an abundance of large cetaceans. The presence of large amounts of lipids in the bones showed that the carcass was still able to support life on the seafloor even after a considerable time, and the diverse faunal assemblage found on this skeleton included several undescribed species.

Tuesday, July 30, 2013

A video by the University of Guelph SPARK team. SPARK is a training opportunity at UofG for students to gain experience in media communications. In over 20 years it made science understandable to the public and helped develop a culture that is supportive of research.

This video is a nice intro to DNA Barcoding and the work that is done here at our institute. It was published for the opening ceremony of the new building addition here at BIO, the Centre for Biodiversity Genomics.

Monday, July 29, 2013

Psocids (Psocoptera) are small, soft-bodied insects and are now considered significant pests of stored products. They can persist on a variety of foods, and there is variation in biology and ecology among the different species. Psocids are tiny insects that live in damp environments where they eat mold and mildew. They are often called bark lice or book lice. The name bark lice probably comes from the fact that they gather under the bark of trees while the name book lice comes from the fact that they gather on moldy books in damp homes. Experts think that the sizing and starch in the bindings of books supports mold growth in humid environments.

The pest status of stored-product psocids is due to the weight losses caused by consumption of germ and endosperm. As a result commodities infected can be rejected for export. They also have the ability to spread fungal pathogens, thereby making them a human health threat especially through allergic responses they cause in sensitized people.

Recent studies have shown psocids to be quite tolerant to some of the currently used insecticides when applied at rates usually effective for control of other stored-product insect pests, such as Coleoptera and Lepidoptera. Most challenges in psocid control stem from the fact that even very similar species differ in their sensitivity to various insecticides. The problem is that morphological identification is extremely difficult, further hampered by the lack of psocid entomological experts. A good example is the the genus Liposcelis that includes 126 valid species. About 10% of those commonly occur in habitats associated with humans and many have been identified as pest species.

A new study now successfully tested the suitability of DNA-based identification for Liposcelis members using 16S rDNA and DNA Barcoding (COI). Although it is not entirely clear to me why there was a need to use two mitochondrial markers for species identification it certainly worked well. Unfortunately, the authors join the increasing number of people calling e.g. 16S-based species identification DNA Barcoding which it isn't. Remember, DNA Barcoding for most animals is done only with COI and the community went through great lengths in order to define such standards. Well, I won't go on too long as the researchers did COI which is in turn very helpful for all other researchers that like to use DNA Barcoding for more targeted pest control. Given that different Liposcelis pest species respond differently to control measures, DNA Barcoding might be the only suitable method to optimize response.

Friday, July 26, 2013

We provide a phylogenetic and population genetic evaluation of the illegal pet and bush meat trade of monitor lizards in the Philippines. We use a molecular dataset assembled from vouchered samples with known localities throughout the country, as a reference for statistical phylogenetic, population genetic, and DNA Barcoding analyses of genetic material obtained during a three year survey of the Manila pet trade. Our results provide the first genetic evaluation of a major Southeast Asian city’s illegal trade in monitors and allow us to establish several important conclusions regarding actual, versus reported, origins of Manila’s black market Varanus. Monitor lizards are clearly transported throughout the archipelago for trade; we identified genotypes from areas surrounding Manila, the distinct Bicol faunal subregion of Luzon, Mindanao Island, the Visayan islands, islands of the Romblon Province, the Babuyan islands, and Mindoro Island. Numerous species are involved, including multiple endemic Philippine taxa, the threatened Gray’s monitor (Varanus olivaceus), and the presumably non-Philippine rough-neck monitor (Varanus rudicollis). Our results suggest that traders frequently and deliberately misrepresent the provenance of traded animals, in an apparent effort to increase their perceived market value.

This is the abstract of a study published this year in Biological Conservation. This study is just a snapshot of the conservation crisis of Southeast Asian wildlife caused by illegal trade. An increasing number of vertebrates are removed from their natural habitats, harvested for both legal and illegal trade in skins, bush meat, exotic pets, good luck charms, and traditional medicines. The tasks of monitoring the trade as well as illegal shipments have become very difficult. An arms race between illegal dealers and wildlife law enforcement officials is on. Unfortunately the current winners of this race are the smugglers. But there is hope:

Trade forensics has come to represent an increasingly diverse and powerful suite of technological, methodological, and analytical tools and resources for identifying trade species and, hopefully, pinpointing their origins. Although accurate identification of trade animals is accompanied by numerous logistic and biosecurity challenges, determining origins of confiscated animals may help identify trade routes and populations at risk from heavy exploitation pressures. Importantly, our ability to identify actual geographic origins of trade animals with molecular techniques (and reference databases of densely sampled wild-caught animals from known localities) may eventually prove to be a strong deterrent if illegal traders become aware of these new, sophisticated forensic and law enforcement tools.

It is good to see that studies like this one use a suite of methods (phylogenetic, population genetic network, and DNA Barcoding) to identify the provenance of trade animals, and compare those information to those reported by traders and dealers. Although the researchers focused only on one commercial hub of the monitor lizard trade, the pet markets in and around metro Manila, Philippines, they could show that the combined approach allowed assignment of samples to species but also to particular islands or subregions on larger islands. So, indeed good news that again proof the value of modern genetic methods but:

Numerous additional, unrelated taxa should now be similarly studied; the Manila pet trade regularly deals in a wide variety of amphibians, reptiles, birds, mammals, and marine fish. Additionally, phyloforensic monitoring of the illegal Philippine pet trade should focus on the numerous well-developed trade centers we are aware of on Palawan (Puerto Princesa City), Cebu (Cebu City), and Mindanao (Davao City) islands, as well as many smaller cities on Luzon Island (personal observations). Many of these clearly are the conduits through which animals enter the Philippines from other countries, as well as sources for illegal smuggling of animals to regions outside of the Philippines. Finally, in many rural provinces in the Philippines, thriving local bush meat markets deal in wild caught forest species. We anticipate that most of these will be found to deal in species from areas in close proximity to these smaller local markets, but this speculation remains to be tested. In addition to the necessity of widespread geographic and taxonomic sampling to combat illegal trade in the Philippines, such efforts should be extended to countries where illegal trade in animals is of similar concern. Much of Southeast Asia, central Africa, Australia, and northern South America have been plagued by circumstances similar to those found in the Philippines. These regions are home to species which are highly sought after in the pet, traditional medicine, and skin trades, and should be targeted for widespread sampling of natural populations in order to asses those populations most at risk and severely threatened by illegal exploitation.

Friday, July 19, 2013

Today an exclusive preview of the program for the 5th International Barcode of Life Conference in Kunming (27-31. Oct 2013). Over the next couple of days the conference website will be updated quite a bit and more detailed calls for participation and abstracts will go out to everyone. I'll keep you posted on all new developments via this blog as well. Stay tuned and you won't miss any news!

Conference Sessions

All conference sessions will be held at the Lian Yuan Hotel in Kunming.

Preliminary Conference Schedule - 5th International Barcode of Life Conference

Parallel Sessions - Expected Themes

The following are expected themes for the parallel sessions. Please contact us as soon as possible if there is a theme that you would like to see added and/or moderate that is not included in the list below.

Wednesday, July 17, 2013

Do you cook? Of course I mean real cooking not heating up a pre-processed meal. I love cooking from scratch and use fresh and largely unprocessed ingredients. In this regard you might understand my fondness for olive oil. To me it tastes better than many other oils and it also has been associated with a lot of health beneﬁts. Preliminary clinical studies have provided evidence that consumption of olive oil may lower the risk of heart disease through factors such as lower blood cholesterol levels and reduced LDL cholesterol oxidation. Pilot studies also showed that olive oil may affect oxidative damage to DNA and RNA, revealing a possible carcinogenic factor.

Such benefits make good olive oil more expensive than other vegetable oils which unfortunately makes it particularly prone to fraudulent practices. It is frequently blended with lower-cost oils of plant origin, such as soya (Glycine max), canola (Brassica napus), maize (Zea mays), sunﬂower (Helianthus annuus), and even sesame (Sesamum indicum) oils.

So far adulteration of plant oils was mainly determined with analytical chemistry methods with limits of detection of around 5%. There is a clear need for a reliable, more sensitive method to detect the botanical origin of oils and oil mixtures. To me this sounds like a case for DNA Barcoding and indeed some researchers from Greece have put it to the test. They explicitly tested a high-resolution melting analysis-based method (HRM) using the rbcL barcoding region as target to obtain barcoding references for the major vegetable oil species and to quantitatively identify the botanical origin of plant oils. They also tested various mixtures of olive and canola oil to demonstrate the applicability of HRM for the detection of adulterants. The new method was capable both of distinguishing among different vegetable oil species and detecting a level of 1% of canola oil in olive oil.

Very promising and given the relatively low cost of HRM methods very reassuring as this method could be easily adopted in regular food inspections. I very much like the idea of having good and more importantly pure olive oil in our meals. And by the way - always use cold pressed extra virgin ones.

Tuesday, July 16, 2013

Over the years I have been part of the marine barcoding movement I always thought: " Folmer et al. must have been damn lucky!" That does not at all devalue the work of these researchers back in 1994. Until today their primers have been used with many organisms in order to retrieve a COI fragment that 9 years after the primer was developed was declared the DNA Barcode region for animals. However, these primers are not really universal in applicability. The so called Folmer primers often fail or perform poorly. A large range of especially marine invertebrates can't be sequenced with them. Unfortunately, the general reaction to the problem was to develop more taxon specific primers and adapt laboratory protocols accordingly. Nevertheless real universal primers were always deemed desirable.

Now it seems we do have a new set that would be ready to do the job. Maybe not across all animal life but at least for the large fraction that lives in the ocean and has no backbone. US researchers have now published a set of new primers, called jgHCO2198 and jgLCO1490, which are well suited for routine DNA barcoding, all-taxon surveys and metazoan metagenomics.

Although I am truly happy about this advance to which I can congratulate the authors I have two issues with the paper and both relate to data sharing and open access.

Number one is a more general one and not necessarily criticism of this particular paper alone. Why does the scientific community always have to wait years before such breakthroughs are shared and primer sequences published? I don't see the point why primers are not shared right after they have been developed. Their success is perhaps not guaranteed but sharing them in some sort of a general database would largely increase the number of experiments and provide researchers with results that in turn show them how universal or specific their newly designed oligo is.

It is a shame that for most primers we still have to wait for the associated publication to come out before we 'discover' them. I wonder how many primer combinations have been repeatedly developed independent from each other. What a waste of precious time and only because we are still largely paranoid and self-serving in our community. I am not excluding myself from this as I am also guilty of holding back such information for years waiting for all results to come in to write the big paper that gives me the impact factor I thought I deserve. Well, that nonsense is over. A few years back I decided to apply the open access concept to the few primers I developed for DNA Barcoding. Those are at least available through the BOLD primer database. They might never end up in a publication. I don't see a problem in releasing them before a paper is submitted.

So, why don't we just put primers up as soon as we designed them? There are a couple of databases out there although none of them has a community interface that would allow feedback on success. At least for primers relevant to the DNA Barcoding community BOLD could extend their interface. Just a thought.

My second major criticism is summarized in one question: Where are the sequences relating to this paper? Some 7600 sequences of marine invertebrates have been recovered using this new primer set but why are they not shared via GenBank or BOLD? This is an old problem in the entire DNA Barcoding movement. There is a barcoding twilight zone and its proportions are largely unknown. It is home to sequences that reside on individual researchers hard disks or institutional databases. Both are locked up and the community can only hope that some day the data will be released. This seriously hampers any effort to effectively build DNA Barcode libraries as nobody really knows what has been sequenced and what not. The best solution to this problem is the paradigm shift many people silently hope for - full immediate data release that also allows for community tagging and commenting as realized in BOLD. Unfortunately, there are also many people that rather like to lock up their data indefinitely to make sure that everything is correct before releasing. They are concerned to spread partially erroneous data. Understandable point but it is the typical Wikipedia counterargument. I think we researchers should start to embrace community approaches out there. Say what you will - Wikipedia got better with the number of contributors especially the ones that do a proper job. Time to do the same and stop sitting on data.

Monday, July 15, 2013

Researchers from the University of Alaska Fairbanks discovered a strange new insect on Prince of Wales Island, Alaska. It belongs to an enigmatic group that might help understand the evolutionary origin of the fleas. The new species belongs to the insect order Mecoptera which includes the scorpionflies, hangingflies, and snow scorpionflies.

"We process thousands of Alaskan insects specimens into our collections at the University of Alaska Museum every year so it's rare that we see something that throws us for a loop. I called Derek, the Curator of Insects for the museum, into the lab and asked him what kind of insect this was and he didn't even know the order!," said co-author Jill Stockbridge.

They posted an image of the animal on Facebook so their entomologist colleagues could offer their opinions. It's such a strange insect that, not surprisingly, most suggestions were wrong. One entomologist, Michael Ivie, of Montana State University, recognized it as the genus Caurinus of which only one species, from Washington and Oregon, was previously known.

"In addition to being the second known species of such an usual group of insects, we were excited to learn from fossil evidence that these two species belong to a group that probably dates back over 145 million years, to the Jurassic!" said the lead author Derek Sikes.

These tiny (2 mm) flea-like animals feed on a leafy liverwort that grows in coastal forests. A video in which Loren Russell, the author of the first species and who joined the authors during a May 2013 expedition in Alaska, shows how to collect this new species:

Friday, July 12, 2013

Smart drugs or better known as ‘legal highs’ are substances which produce similar effects to illegal drugs (such as cocaine, cannabis and ecstasy) but are not controlled under any drug legislation. These new substances are not yet controlled because there is not enough research about them yet to ban. The products are available in a variety of forms, e.g. some herbal smoking mixes are marketed as legal alternatives to cannabis and consist of plants rich in alkaloids or stimulant substances. On the other hand, some herbal mixtures also contain added synthetic cannabinoids. The plant ingredients serve as “shuttle,” hiding illegal chemicals and allowing them to be transported and marketed through different channels.

Authorities are seeing an increasing use of synthetic drugs which are disguised as bath salts, potpourri, incense, foods of plant origin, and other products. Currently most of these drugs are not illegal because manufacturers are changing the chemical makeup to achieve an alteration wide enough to avoid legal restriction. For example, in many Western European countries, products known as “Spice” and analogous herbal blends are sold as incense not suitable for human consumption; however, they are normally smoked as drugs, much like cannabis. Only recently, a number of countries in Europe, as well as the USA and Canada, have banned the use of these substances. However, the main problem concerning these herbal blends lies in their identification.

A group of Italian researchers has now combined DNA Barcoding, morphology and high-performance liquid chromatography to identify both the plant and the chemical composition of some last-generation legal highs. The combination of morphological and DNA Barcode data revealed a mixture of plants from different families, including aromatic species representatives of Lamiaceae and Turneraceae that are not known to have any 'drug-like' effects. Furthermore the chemical analyses of extracts showed the presence of synthetic cannabinoids indicating that the plant material was indeed used as 'shuttle' for regulated chemicals.

Another very interesting example of creative ways to use DNA Barcoding.

Thursday, July 11, 2013

Frequent users of the DNA Barcoding platform BOLD know them already - Barcode Index Number's or short, BINs. BOLD features BIN pages already for a while and I know from my own work with a multitude of projects in this system how helpful they can be. Communication with colleagues working on the same set of species has become so much easier because we are operating on the same platform that provides us with all relevant information on a single web page. A BIN page is often the starting point of extensive communication resulting in corrections or revisions mostly coming from taxonomic discordance discovered through BINs. Aside from representing a new algorithm to assign individuals to an operational group this system simply represents the best collaborative tool in biodiversity science and taxonomy that there is at this point.

It took a bit to publish a paper which summarizes both the underlying algorithm and database structure as well as the utilization on BOLD. However, after a first read of the publication I would say it was worth the wait. As a reaction to this publication Rod Page said on his blog: Might be time to revisit the dark taxa idea.

You want to know more? I think I let the authors speak for themselves. Here is the abstract:

Because many animal species are undescribed, and because the identification of known species is often difficult, interim taxonomic nomenclature has often been used in biodiversity analysis. By assigning individuals to presumptive species, called operational taxonomic units (OTUs), these systems speed investigations into the patterning of biodiversity and enable studies that would otherwise be impossible. Although OTUs have conventionally been separated through their morphological divergence, DNA-based delineations are not only feasible, but have important advantages. OTU designation can be automated, data can be readily archived, and results can be easily compared among investigations. This study exploits these attributes to develop a persistent, species-level taxonomic registry for the animal kingdom based on the analysis of patterns of nucleotide variation in the barcode region of the cytochrome c oxidase I (COI) gene. It begins by examining the correspondence between groups of specimens identified to a species through prior taxonomic work and those inferred from the analysis of COI sequence variation using one new (RESL) and four established (ABGD, CROP, GMYC, jMOTU) algorithms. It subsequently describes the implementation, and structural attributes of the Barcode Index Number (BIN) system. Aside from a pragmatic role in biodiversity assessments, BINs will aid revisionary taxonomy by flagging possible cases of synonymy, and by collating geographical information, descriptive metadata, and images for specimens that are likely to belong to the same species, even if it is undescribed. More than 274,000 BIN web pages are now available, creating a biodiversity resource that is positioned for rapid growth.

Monday, July 8, 2013

Last Thursday close to the small dutch village of Luttelgeest animal body remains were discovered. So far the species identity is not clear and there are chances that this could be the first wolf encounter in the Netherlands in 150 years.

Several press releases reported that the researchers will confirm the species identity with DNA Barcoding. I have to admit that I have my doubts about that. There were no details on how the carcass looked like but some articles claim that the animal was likely killed the night before it was found which means the body is rather intact. The only other animal that comes to mind is a dog which is the same species, Canis lupus. Many consider the dog as a subspecies. As I am not a firm believer in any subspecies concept I consider them members of the same species, one of them - the wolf - being the ancestral form, the other the product of artificial selection.

A quick look on BOLD shows that COI is ill-equipped to distinguish between dog and wolf. My best bet would be the use of short tandem repeat (STR) markers that have variants specific to wolves and Single Nucleotide Polymorphisms (SNPs) to compare with certain dog breeds that are commonly used to produce hybrids. Such population assignments and admixture analyses determine the likelihood that the subject animal is a dog, wolf or even a hybrid.

Undoubtedly a perhaps very exciting find but it is not a case were DNA Barcoding can help with. Actually if the carcass is not damaged too much it should be possible for an expert mammalogist to identify the species based on good old morphology.

Currently we are in the middle of presentations of the partner nations. The photo shows Axel Hausmann presenting Germany's projects. I'll do my best to play live-reporter from the event via blog and twitter. Later the day we also celebrate the grand opening of our large building extension, called Centre for Biodiversity Genomics (CBG). More on that later. Stay tuned...

Wednesday, July 3, 2013

Plants that emit an airborne distress signal in response to herbivory may actually attract more enemies, according to a new study published by a team of researchers from Switzerland. They found that the odor released by maize plants under attack by insects attract not only parasitic wasps, which prey on herbivorous insects, but also caterpillars of the Egyptian cotton leafworm moth Spodoptera littoralis, a species that feeds on maize leaves.

When damaged, many plants release volatile organic compounds, similar to the compounds that cause the characteristic smell of freshly cut grass. These compounds are known to be attractive to parasitoid wasps that lay their eggs inside other insects. Plants appear to use this strategy to fight back against herbivorous insects by calling for their enemies' enemies. In contrast, herbivorous insects such as adult moths and butterflies tend to avoid food plants that are under attack by conspecifics. However, Spodoptera littoralis caterpillars are actually attracted to the odor of damaged maize plants, even when this odor is mimicked in the laboratory with a mix of synthetic compounds

To determine what kind of odors the caterpillars preferred, the researchers let the caterpillars chose among several odors by placing them in an olfactometer, a device consisting of tubes connected to a central chamber, with each tube introducing an airflow carrying a different odor. The caterpillars were more than twice as likely to crawl towards the odor from maize plants under attack by conspecifics than towards undamaged plants, especially if the damage was recent and the caterpillars had already fed on maize.

The question is what might be the advantage to the caterpillars of moving towards plants that are already infested also given the risk of being attacked by parasitoid wasps. The advantage seems to be that fallen caterpillars can quickly rediscover the plant on which they fed by moving towards volatile organic compounds released by damaged maize plants. When they drop from a plant they become highly vulnerable to predators and pathogens in the soil, as well as to starvation. On damaged plants the competition may be more intense, but at least the caterpillars are assured of a suitable plant. The team also observed that the caterpillars feed less and move more when exposed to high concentrations of the volatiles. By moving away from freshly damaged sites, they can minimize risk of predation and avoid competition.

Adult moths, on the other hand, are much more mobile and explore the environment to discover the best food source. As a result they avoid maize that is already under attack

Tuesday, July 2, 2013

Two more cases of fish mislabeling hit the press this past weekend. Not that this is something new. We did quite a few studies in the past 5 years here in Guelph and we are not the only lab conducting those. However, given how frequent this bad habit is, it seems that both consumers and inspection authorities need equally frequent reminders. So here we go:

4 out of 15 samples were wrongly labelled although two of them might have been clerical errors. Antarctic toothfish (Dissostichus mawsoni) was sold as Patagonian toothfish (Dissostichus eleginoides). The latter is often marketed as Chilean Sea Bass which is sanctioned by the US FDA. Both Dissostichus species have overlapping distributions and this case could be a simple mistake by the fisherman. Nevertheless, it is still not legal.

The second study was conducted in Italy and is even more concerning as it looked at the local fish market in Milan. Researchers from the University of Milan, Bicocca collected dogfish samples from 45 shops in Milan. In 85% cases samples were not dogfish at all. They mostly found 15 species that were not even on the commercial lists. Every month up to 20 tons of dogfish are sold in Milan alone. The price is around 15 Euros a kilo but the substitutes found are mostly worth less than 5 Euros. But there were also protected and endangered species among the samples. In one instance the team found great white shark.